3WGY

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with 4-methyl-2-oxovalerate of from Clostridium tetani E88

• PDB DOI: https://doi.org/10.2210/pdb3WGY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium tetani E88
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-19 Released: 2014-08-20 
• Deposition Author(s): Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 

Literature

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with 4-methyl-2-oxovalerate of from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.7 kDa 
• Atom Count: 5,961 
• Modelled Residue Count: 647 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meso-diaminopimelate dehydrogenase	A, B	326	Clostridium tetani E88	Mutation(s): 6  Gene Names: CTC_02532, meso-dapdh EC: 1.4.1.16
UniProt
Find proteins for Q890V3 (Clostridium tetani (strain Massachusetts / E88)) Explore Q890V3  Go to UniProtKB:  Q890V3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COI	C [auth B]	2-OXO-4-METHYLPENTANOIC ACID C6 H10 O3 BKAJNAXTPSGJCU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.191	α = 90
b = 135.536	β = 110.54
c = 60.792	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations